Hello GATK Team,
The documentation entitled 'When HaplotypeCaller and Mutect2 do not call an expected variant' suggests running Mutect2 with the argument --debug-graph-transformations set as true as a later option in troubleshooting for the issue discussed in this documentation. However, this argument is not available in later versions of Mutect2, including the current version.
Which argument(s) should be used instead (e.g. --assembly-region-out, --debug-assembly, --graph-output, --pair-hmm-results-file)? Should .dot files still be generated?
Thank you for your time and help.
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